inherits(pyr, "pyranges.pyranges.PyRanges") is not TRUE

[vinodsinghjnu]

Can anybody tell what type of error this is, on a given test example?

> use_python("/home/xx/miniforge3/envs/R.4.2_cloned_mapdemo_env/bin/python3")
> gr <- GRanges("chr1", IRanges(1:3, 20))
> pyr <- makePyRangesFromGRanges(gr)
> pyr  # PyRanges objects follow the 0-based start convention!!

+--------------+-----------+-----------+
| Chromosome   |     Start |       End |
| (category)   |   (int64) |   (int64) |
|--------------+-----------+-----------|
| chr1         |         0 |        20 |
| chr1         |         1 |        20 |
| chr1         |         2 |        20 |
+--------------+-----------+-----------+

> makeGRangesFromPyRanges(pyr)

Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes.
For printing, the PyRanges was sorted on Chromosome.
Error in makeGRangesFromPyRanges(pyr) : 
 inherits(pyr, "pyranges.pyranges.PyRanges") is not TRUE

[hpages]

Can't reproduce this:

library(BiocPyRanges)

gr <- GRanges("chr1", IRanges(1:3, 20))
pyr <- makePyRangesFromGRanges(gr)

class(pyr)
# [1] "pyranges.pyranges.PyRanges" "python.builtin.object"     

inherits(pyr, "pyranges.pyranges.PyRanges")
# [1] TRUE

makeGRangesFromPyRanges(pyr)
# GRanges object with 3 ranges and 0 metadata columns:
#       seqnames    ranges strand
#          <Rle> <IRanges>  <Rle>
#   [1]     chr1      1-20      *
#   [2]     chr1      2-20      *
#   [3]     chr1      3-20      *
#   -------
#   seqinfo: 1 sequence from an unspecified genome; no seqlengths

What versions of pyranges + pandas are you using and what's your sessionInfo()? See mines below.

Best,
H.

> subset(py_list_packages(), package %in% c("pandas", "pyranges"))
    package version       requirement
77   pandas   1.5.3     pandas==1.5.3
92 pyranges 0.0.111 pyranges==0.0.111

sessionInfo():

R version 4.3.0 Patched (2023-05-31 r84481)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 23.04

Matrix products: default
BLAS:   /home/hpages/R/R-4.3.r84481/lib/libRblas.so 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] BiocPyRanges_0.0.1   GenomicRanges_1.52.0 GenomeInfoDb_1.36.1 
[4] IRanges_2.34.1       S4Vectors_0.38.1     BiocGenerics_0.46.0 
[7] reticulate_1.31     

loaded via a namespace (and not attached):
 [1] zlibbioc_1.46.0         Matrix_1.6-0            lattice_0.21-8         
 [4] GenomeInfoDbData_1.2.10 XVector_0.40.0          RCurl_1.98-1.12        
 [7] png_0.1-8               bitops_1.0-7            cli_3.6.1              
[10] grid_4.3.0              compiler_4.3.0          tools_4.3.0            
[13] Rcpp_1.0.11             rlang_1.1.1             jsonlite_1.8.7         

[vinodsinghjnu]

Thankyou Hervé Pagès, for your quick response and putting your efforts to a tool that have huge opportunities.

Here are my details of the code and R environment. Please note that I am running R under conda environment

> use_python("/home/xx/miniforge3/envs/R.4.2_cloned_mapdemo_env/bin/python3")
> gr <- GRanges("chr1", IRanges(1:3, 20))
> pyr <- makePyRangesFromGRanges(gr)
> makeGRangesFromPyRanges(pyr)
Error in makeGRangesFromPyRanges(pyr) : 
  inherits(pyr, "pyranges.pyranges.PyRanges") is not TRUE
> 
> class(pyr)
[1] "pyranges.pyranges_main.PyRanges" "python.builtin.object"          
> inherits(pyr, "pyranges.pyranges.PyRanges")
[1] FALSE
> 
> subset(py_list_packages(), package %in% c("pandas", "pyranges"))
     package version      requirement     channel
173   pandas   2.0.3     pandas=2.0.3 conda-forge
202 pyranges 0.0.129 pyranges=0.0.129        pypi
> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/xx/miniforge3/envs/R.4.2_cloned_mapdemo_env/lib/libopenblasp-r0.3.23.so

locale:
 [1] LC_CTYPE=en_US.utf-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.utf-8        LC_COLLATE=en_US.utf-8    
 [5] LC_MONETARY=en_US.utf-8    LC_MESSAGES=en_US.utf-8   
 [7] LC_PAPER=en_US.utf-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.utf-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] BiocPyRanges_0.0.1   GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 
[4] IRanges_2.32.0       S4Vectors_0.36.2     BiocGenerics_0.44.0 
[7] reticulate_1.30     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.11            here_1.0.1             lattice_0.21-8        
 [4] png_0.1-8              rprojroot_2.0.3        withr_2.5.0           
 [7] rappdirs_0.3.3         bitops_1.0-7           grid_4.2.3            
[10] jsonlite_1.8.7         zlibbioc_1.44.0        rlang_1.1.1           
[13] cli_3.6.1              XVector_0.38.0         Matrix_1.6-0          
[16] tools_4.2.3            RCurl_1.98-1.12        compiler_4.2.3        
[19] GenomeInfoDbData_1.2.9

[hpages]

Looks like you're using a more recent version of the pyranges module (0.0.129, the latest).

So it seems that, back in April, the pyranges folks renamed the pyranges.pyranges submodule -> pyranges.pyranges_main (see pyranges/pyranges0@74901aa). The change happened in pyranges 0.0.120, but, surprisingly, such breaking change is not mentioned in the CHANGELOG.txt file (see https://github.com/pyranges/pyranges/blob/master/CHANGELOG.txt).

The consequence of this change is that the class of the object returned by makePyRangesFromGRanges() is now pyranges.pyranges_main.PyRanges (like in your case), whereas before that it was pyranges.pyranges.PyRanges (like in my case).

I commited a small tweak to BiocPyRanges to accomodate for this change (see commit 9c7fb50). The fix is in BiocPyRanges 0.0.2. Let me know if you still run into issues with this new version.

Best,
H.